A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/rnavar analysis pipeline. For information about how to interpret these results, please see the documentation.
/work/user/fmt116/TP_nextflow/projet_nextflow/sra_tools/work/ba/4a8f4227590dc4822d79aeb5e47ff1
General Statistics
| Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Duplication |
|---|---|---|---|---|---|---|---|
| SRR2045415 | 22.4M | 20.1M | 89.6% | 19.1M | 85.3% | 1.0M | 21.8% |
| SRR2045416 | 36.5M | 28.2M | 77.4% | 27.4M | 75.1% | 0.8M | 11.2% |
Read Alignment (STAR)
Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635
Summary Statistics
Summary statistics from the STAR alignment
| Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Avg. read len | Avg. mapped len | Splices | Annotated splices | GT/AG splices | GC/AG splices | AT/AC splices | Non-canonical splices | Mismatch rate | Del rate | Del len | Ins rate | Ins len |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR2045415 | 22.4M | 20.1M | 89.6% | 19.1M | 85.3% | 1.0M | 200.0bp | 197.3bp | 16.6M | 16.5M | 16.3M | 0.2M | 0.0M | 0.1M | 0.9% | 0.0% | 2.3bp | 0.0% | 1.9bp |
| SRR2045416 | 36.5M | 28.2M | 77.4% | 27.4M | 75.1% | 0.8M | 200.0bp | 196.9bp | 15.4M | 15.4M | 15.2M | 0.1M | 0.0M | 0.1M | 1.0% | 0.0% | 2.4bp | 0.0% | 1.9bp |
Alignment Scores
Samtools Flagstat
Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352
Mapped reads per contig
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
GATK4 MarkDuplicates
Metrics generated either by GATK4 MarkDuplicates.URL: http://broadinstitute.github.io/picard
Mark Duplicates
Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.
The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.
To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:
READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATESREADS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATESREADS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATESREADS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICALREADS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATESREADS_UNMAPPED = UNMAPPED_READS
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| CAT_FASTQ | cat | 9.5 |
| FASTQC | fastqc | 0.12.1 |
| GATK4_BEDTOINTERVALLIST | gatk4 | 4.6.1.0 |
| GATK4_CREATESEQUENCEDICTIONARY | gatk4 | 4.6.1.0 |
| GATK4_HAPLOTYPECALLER | gatk4 | 4.6.1.0 |
| GATK4_INTERVALLISTTOOLS | gatk4 | 4.6.1.0 |
| GATK4_MERGEVCFS | gatk4 | 4.6.1.0 |
| GATK4_SPLITNCIGARREADS | gatk4 | 4.6.1.0 |
| GATK4_VARIANTFILTRATION | gatk4 | 4.6.1.0 |
| GTF2BED | Rscript | 3.5.1 (2018-07-02) |
| PICARD_MARKDUPLICATES | picard | 3.3.0 |
| REMOVE_UNKNOWN_REGIONS | python | 3.8.3 |
| SAMTOOLS_FAIDX | samtools | 1.21 |
| SAMTOOLS_IDXSTATS | samtools | 1.21 |
| SAMTOOLS_INDEX | samtools | 1.21 |
| SAMTOOLS_MERGE | samtools | 1.21 |
| SAMTOOLS_SORT | samtools | 1.21 |
| SAMTOOLS_STATS | samtools | 1.21 |
| STAR_ALIGN | gawk | 5.1.0 |
| samtools | 1.21 | |
| star | 2.7.11b | |
| STAR_INDEXVERSION | gawk | 5.1.0 |
| samtools | 1.21 | |
| star | 2.7.11b | |
| Samtools Flagstat | samtools | 1.21 |
| TABIX | tabix | 1.21 |
| Workflow | Nextflow | 25.04.0 |
| nf-core/rnavar | v1.2.1-g2cbf046 |